Mouse H 1.11 homeobox DNA was cloned and sequenced. Hox 1.11 poly A+ RNA is expressed in 12 to 14 day-old mouse embryos in the hind brain up to, but not including, the pons. Hox 1.11 poly A+ RNA also was expressed in the spinal cord, the VIIth and VIIIth cranial ganglia, spinal ganglia, larynx, lungs, vertebrae, sternum, and intestine. A mouse homeobox gene, mNK-1, was cloned and approximately 5.2 kb of DNA was sequenced. Comparison of the amino acid sequences of the mouse and Drosophila NK-1 revealed 95% homology. Hox 4.1 cDNA and genomic DNA were cloned and sequenced; comparison of Hox 4.1 and Hox 2.7 proteins revealed 59% homology. Hox 4.9 also was cloned and partially sequenced. Four Pou-domain genes expressed in embryonic and adult mouse brain were cloned and sequenced; Brain-1, Brain-2, Brain-4, and Scip. Similar amino acid sequences were found in various regions of the proteins. No introns were detected in the coding regions of the 4 Pou-domain genes which suggests that the genes originated by reverse transcriptions of an ancestral species of Pou-domain mRNA followed by insertion of cDNA molecules into germ cell DNA. The Drosophila homeobox gene, NK-2, is expressed initially by virtually all cells in the ventral neurogenic anlage as the neurogenic anlage appears. The nucleotide sequence of the DNA binding site for the NK-2 homeodomain was determined. Putative genes that are regulated by NK-2 protein were cloned and were sequenced partially. Drosophila genomic DNA corresponding to 20 genes identified in enhancer trap experiments, which for the most part are expressed specifically in the nervous system, were cloned. A nuclear protein was found that binds to a novel trinucleotide repeat sequence in the 5'-upstream region of a rat brain voltage-sensitive calcium channel alpha1 subunit that activates an enhancerless chloramphenicol acetyltransferase reporter gene. cDNA clones were obtained that encode 3 kinds of DNA binding proteins, each specific for a different novel mouse enhancer sequence were cloned.